TB-Profiler result

Run: ERR9806995
Summary

Run ID: ERR9806995

Sample name:

Date: 18-05-2023 20:52:28

Number of reads: 2812480

Percentage reads mapped: 99.56

Strain: lineage2.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol
Pyrazinamide R pncA p.Tyr103* (1.00)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethR p.Ala95Thr (0.95)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288933 p.Tyr103* stop_gained 1.0 pyrazinamide
ethR 4327831 p.Ala95Thr missense_variant 0.95 ethionamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 5443 c.204G>A synonymous_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9359 c.2058C>T synonymous_variant 0.12
fgd1 490641 c.-142G>A upstream_gene_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575540 p.Ala65Ser missense_variant 0.11
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.95
rpoB 760761 p.Gly319Ser missense_variant 0.12
rpoB 761577 c.1772delT frameshift_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 764300 p.Gly311Cys missense_variant 0.22
rpoC 766488 p.Pro1040Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303637 p.Lys236Arg missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407495 c.-155C>T upstream_gene_variant 0.14
embR 1417303 c.45G>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472724 n.879G>T non_coding_transcript_exon_variant 0.2
fabG1 1674058 p.Pro207Thr missense_variant 0.13
inhA 1674208 p.Gly3Arg missense_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102133 p.Gln304* stop_gained 0.12
ndh 2102138 p.Arg302Leu missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155738 p.Gly125Asp missense_variant 0.17
PPE35 2167877 c.2736C>T synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289032 c.210G>A synonymous_variant 0.14
kasA 2519082 p.Ala323Asp missense_variant 0.14
kasA 2519159 p.Ala349Thr missense_variant 0.12
folC 2746185 p.Val472Leu missense_variant 0.15
folC 2747309 p.Thr97Asn missense_variant 0.13
Rv2752c 3065728 p.Ala155Val missense_variant 0.14
thyX 3068103 c.-158C>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087228 p.Ala137Ser missense_variant 0.13
fbiD 3339604 p.Gly163Trp missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474229 p.Arg75Ser missense_variant 0.25
fprA 3474884 p.Glu293Gly missense_variant 0.12
fprA 3474914 p.Ala303Val missense_variant 0.12
fprA 3475032 c.1026C>A synonymous_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640721 p.Pro60Gln missense_variant 0.14
fbiB 3641887 p.Leu118Ser missense_variant 0.11
alr 3840314 c.1107C>T synonymous_variant 0.12
rpoA 3877977 p.Lys177Asn missense_variant 0.12
panD 4044313 c.-32C>A upstream_gene_variant 0.12
panD 4044406 c.-125C>A upstream_gene_variant 0.12
embC 4240630 c.768C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243439 c.207G>A synonymous_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248527 p.Phe672Leu missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338318 c.203delA frameshift_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0